This is a presentation¶
B cell progenitor CD14+ Monocytes CD16+ Monocytes
522 3369 461
CD4 Memory CD4 Naive CD8 effector
2227 1952 755
CD8 Naive Dendritic cell Double negative T cell
1297 133 147
NK cell pDC Platelets
477 114 2
pre-B cell
453
CD14+ Monocytes CD16+ Monocytes Lymphoid Platelets
3369 461 8077 2
B cell progenitor CD14+ Monocytes CD16+ Monocytes
636 4032 506
CD4 Memory CD4 Naive CD8 effector
1999 1549 747
CD8 Naive Dendritic cell Double negative T cell
1069 131 138
NK cell pDC Platelets
458 126 5
pre-B cell
620
CD14+ Monocytes CD16+ Monocytes Lymphoid Platelets
4032 506 7473 5
Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.
UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()...
UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()...
UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()... UMAP embedding was not computed. Running run_umap()...
Warning message:
"The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session"
Warning message:
"Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
Please use `as_label()` or `as_name()` instead.
This warning is displayed once per session."
Error in eval(expr, envir, enclos): object 'gsea.positive' not found Traceback:
Intersecting features names in the model and the gene set annotation results in a total of 7281 features. Running feature set Enrichment Analysis with the following options... View: ATAC_distal Number of feature sets: 633 Set statistic: mean.diff Statistical test: parametric Subsetting weights with positive sign Intersecting features names in the model and the gene set annotation results in a total of 7281 features. Running feature set Enrichment Analysis with the following options... View: ATAC_distal Number of feature sets: 633 Set statistic: mean.diff Statistical test: parametric Subsetting weights with negative sign
Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message in get0(oNam, envir = ns): “internal error -3 in R_decompress1”
Error: .onLoad failed in loadNamespace() for 'checkmate', details:
call: get0(oNam, envir = ns)
error: lazy-load database '/usr/local/lib/R/site-library/backports/R/backports.rdb' is corrupt
Traceback:
1. Signac::RunChromVAR
2. getExportedValue(pkg, name)
3. asNamespace(ns)
4. getNamespace(ns)
5. loadNamespace(name)
6. namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
. .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
7. asNamespace(ns)
8. loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
9. namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
. .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
10. asNamespace(ns)
11. loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
12. namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
. .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
13. asNamespace(ns)
14. loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
15. namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
. versionCheck = vI[[i]]), from = package)
16. loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
17. runHook(".onLoad", env, package.lib, package)
18. stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s",
. hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L],
. conditionMessage(res)), call. = FALSE, domain = NA)
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing github package(s) 'GreenleafLab/chromVAR' Downloading GitHub repo GreenleafLab/chromVAR@HEAD
BiocParallel (1.24.0 -> 1.24.1) [CRAN] R6 (2.4.1 -> 2.5.0 ) [CRAN] digest (0.6.25 -> 0.6.27) [CRAN] generics (0.0.2 -> 0.1.0 ) [CRAN] cpp11 (0.2.3 -> 0.2.4 ) [CRAN] backports (1.1.10 -> 1.2.0 ) [CRAN] diffobj (NA -> 0.3.2 ) [CRAN] rstudioapi (0.11 -> 0.12 ) [CRAN] waldo (NA -> 0.2.3 ) [CRAN] brio (NA -> 1.1.0 ) [CRAN] colorspace (1.4-1 -> 2.0-0 ) [CRAN] labeling (0.3 -> 0.4.2 ) [CRAN] testthat (2.3.2 -> 3.0.0 ) [CRAN] nabor (NA -> 0.5.0 ) [CRAN]
Installing 14 packages: BiocParallel, R6, digest, generics, cpp11, backports, diffobj, rstudioapi, waldo, brio, colorspace, labeling, testthat, nabor
✔ checking for file ‘/tmp/Rtmptd3t2X/remotesa7225dce/GreenleafLab-chromVAR-0f27fcc/DESCRIPTION’ ─ preparing ‘chromVAR’: ✔ checking DESCRIPTION meta-information ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘chromVAR_1.5.0.tar.gz’
Installation path not writeable, unable to update packages: codetools, KernSmooth, nlme Old packages: 'chromVAR', 'deldir', 'HDF5Array', 'leiden', 'MOFA2', 'patchwork', 'reticulate', 'rhdf5', 'Rhdf5lib', 'Signac', 'xfun'
Warning message in FetchData(object = object, vars = c(dims, "ident", features), : "The following requested variables were not found: MA1636.1, MA0102.4, MA0523.1, MA0768.1"
Error: None of the requested features were found: MA1636.1, MA0102.4, MA0523.1, MA0768.1 in slot data
Traceback:
1. FeaturePlot(sortedSeurat, features = motifs.to.plot, reduction = "umap",
. combine = TRUE)
2. stop("None of the requested features were found: ", paste(features,
. collapse = ", "), " in slot ", slot, call. = FALSE)
R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux bullseye/sid Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.10.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] psych_2.0.9 magrittr_1.5 ggbio_1.38.0 [4] BiocGenerics_0.36.0 msigdbr_7.2.1 ggpubr_0.4.0 [7] Signac_1.0.0 Seurat_3.2.2 reticulate_1.16 [10] purrr_0.3.4 data.table_1.13.2 cowplot_1.1.0 [13] ggplot2_3.3.2 MOFA2_0.99.6 loaded via a namespace (and not attached): [1] rappdirs_0.3.1 SnowballC_0.7.0 [3] rtracklayer_1.50.0 pbdZMQ_0.3-4 [5] GGally_2.0.0 tidyr_1.1.2 [7] bit64_4.0.5 knitr_1.30 [9] irlba_2.3.3 DelayedArray_0.16.0 [11] rpart_4.1-15 RCurl_1.98-1.2 [13] AnnotationFilter_1.14.0 generics_0.0.2 [15] GenomicFeatures_1.42.0 RSQLite_2.2.1 [17] RANN_2.6.1 future_1.20.1 [19] bit_4.0.4 spatstat.data_1.4-3 [21] xml2_1.3.2 httpuv_1.5.4 [23] SummarizedExperiment_1.20.0 assertthat_0.2.1 [25] xfun_0.18 hms_0.5.3 [27] evaluate_0.14 promises_1.1.1 [29] progress_1.2.2 readxl_1.3.1 [31] dbplyr_2.0.0 tmvnsim_1.0-2 [33] igraph_1.2.6 DBI_1.1.0 [35] htmlwidgets_1.5.2 reshape_0.8.8 [37] stats4_4.0.3 ellipsis_0.3.1 [39] RSpectra_0.16-0 corrplot_0.84 [41] dplyr_1.0.2 backports_1.1.10 [43] biomaRt_2.46.0 deldir_0.2-2 [45] MatrixGenerics_1.2.0 vctrs_0.3.4 [47] Biobase_2.50.0 Cairo_1.5-12.2 [49] ensembldb_2.14.0 ROCR_1.0-11 [51] abind_1.4-5 withr_2.3.0 [53] BSgenome_1.58.0 checkmate_2.0.0 [55] sctransform_0.3.1 GenomicAlignments_1.26.0 [57] prettyunits_1.1.1 mnormt_2.0.2 [59] goftest_1.2-2 cluster_2.1.0 [61] IRdisplay_0.7.0 lazyeval_0.2.2 [63] crayon_1.3.4 labeling_0.3 [65] pkgconfig_2.0.3 GenomeInfoDb_1.26.0 [67] nlme_3.1-149 vipor_0.4.5 [69] ProtGenerics_1.22.0 nnet_7.3-14 [71] rlang_0.4.8 globals_0.13.1 [73] lifecycle_0.2.0 miniUI_0.1.1.1 [75] BiocFileCache_1.14.0 rsvd_1.0.3 [77] dichromat_2.0-0 cellranger_1.1.0 [79] ggrastr_0.2.1 polyclip_1.10-0 [81] matrixStats_0.57.0 lmtest_0.9-38 [83] graph_1.68.0 Matrix_1.2-18 [85] ggseqlogo_0.1 IRkernel_1.1.1.9000 [87] carData_3.0-4 Rhdf5lib_1.10.1 [89] zoo_1.8-8 base64enc_0.1-3 [91] beeswarm_0.2.3 ggridges_0.5.2 [93] pheatmap_1.0.12 png_0.1-7 [95] viridisLite_0.3.0 bitops_1.0-6 [97] KernSmooth_2.23-17 Biostrings_2.58.0 [99] blob_1.2.1 stringr_1.4.0 [101] qvalue_2.22.0 parallelly_1.21.0 [103] jpeg_0.1-8.1 rstatix_0.6.0 [105] S4Vectors_0.28.0 ggsignif_0.6.0 [107] scales_1.1.1 memoise_1.1.0 [109] plyr_1.8.6 ica_1.0-2 [111] zlibbioc_1.36.0 compiler_4.0.3 [113] RColorBrewer_1.1-2 fitdistrplus_1.1-1 [115] Rsamtools_2.6.0 XVector_0.30.0 [117] listenv_0.8.0 patchwork_1.0.1 [119] pbapply_1.4-3 htmlTable_2.1.0 [121] Formula_1.2-4 MASS_7.3-53 [123] mgcv_1.8-33 tidyselect_1.1.0 [125] stringi_1.5.3 forcats_0.5.0 [127] askpass_1.1 latticeExtra_0.6-29 [129] ggrepel_0.8.2 grid_4.0.3 [131] VariantAnnotation_1.36.0 fastmatch_1.1-0 [133] tools_4.0.3 future.apply_1.6.0 [135] rio_0.5.16 rstudioapi_0.11 [137] uuid_0.1-4 foreign_0.8-80 [139] lsa_0.73.2 gridExtra_2.3 [141] farver_2.0.3 Rtsne_0.15 [143] digest_0.6.25 BiocManager_1.30.10 [145] shiny_1.5.0 Rcpp_1.0.5 [147] GenomicRanges_1.42.0 car_3.0-10 [149] broom_0.7.2 later_1.1.0.1 [151] RcppAnnoy_0.0.16 OrganismDbi_1.32.0 [153] httr_1.4.2 AnnotationDbi_1.52.0 [155] biovizBase_1.38.0 colorspace_1.4-1 [157] XML_3.99-0.5 tensor_1.5 [159] IRanges_2.24.0 splines_4.0.3 [161] uwot_0.1.8 RBGL_1.66.0 [163] RcppRoll_0.3.0 spatstat.utils_1.17-0 [165] plotly_4.9.2.1 xtable_1.8-4 [167] jsonlite_1.7.1 spatstat_1.64-1 [169] R6_2.4.1 Hmisc_4.4-1 [171] pillar_1.4.6 htmltools_0.5.0 [173] mime_0.9 glue_1.4.2 [175] fastmap_1.0.1 BiocParallel_1.24.0 [177] codetools_0.2-16 lattice_0.20-41 [179] tibble_3.0.4 curl_4.3 [181] ggbeeswarm_0.6.0 leiden_0.3.4 [183] zip_2.1.1 openxlsx_4.2.3 [185] openssl_1.4.3 survival_3.2-7 [187] repr_1.1.0 munsell_0.5.0 [189] rhdf5_2.32.4 GenomeInfoDbData_1.2.4 [191] HDF5Array_1.16.1 haven_2.3.1 [193] reshape2_1.4.4 gtable_0.3.0